Reply to “Comment on ‘Anti-cooperativity in hydrophobic interactions: A simulation study of spatial dependence of three-body effects and beyond’ ” [J. Chem. Phys. <b>116</b>, 2665 (2002)]
Bibliographic record
Abstract
An accurate, physically justifiable procedure for determining zero-PMF baselines is essential in addressing the important issue of anti-cooperativity or cooperativity in hydrophobic interactions. For this purpose, the test-particle insertion technique is less dependent on unproven assumptions than other procedures. Its application is recommended for studies in which the technique is computationally feasible. We agree with Czaplewski et al. that much remains to be learned about hydrophobic interactions nonadditivity, and that sustained efforts are needed to overcome numerical uncertainties in the simulation results reported thus far. Nonetheless, with data available to date, there is apparently stronger support for anti-cooperativity than for cooperativity for a significant fraction of solute configurations of the three-methane system in question. This is illustrated by a reanalysis of a three-methane PMF reported previously by Czaplewski et al. [Protein Sci. 9, 1235 (2000)] in light of the new two-methane PMF presented in their Comment.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.006 | 0.030 |
| Meta-epidemiology (narrow) | 0.002 | 0.002 |
| Meta-epidemiology (broad) | 0.002 | 0.002 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.004 | 0.005 |
| Scholarly communication | 0.002 | 0.004 |
| Open science | 0.006 | 0.003 |
| Research integrity | 0.045 | 0.050 |
| Insufficient payload (model declined to judge) | 0.008 | 0.010 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".